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pyemma-workshop

Installation

We strongly recommend to install the latest pyemma and deeptime release from the anaconda Python distribution.

step 1: Miniconda

If you do not have miniconda or anaconda, please follow the instructions here for Python 3.8: https://conda.io/miniconda.html

We recommend to create a separate environment for the workshop, especially if you already have a anaconda/miniconda installation:

# these steps are optional but recommended
conda create -n workshop
conda activate workshop

# this is not optional
conda config --env --add channels conda-forge

NOTE

For Windows users it makes sense to also install GIT if it is not already available on the system: conda install git

step 2: pyemma and deeptime

Installation of all required software packages works by simply executing:

conda install python=3.9 pyemma_tutorials networkx black

You can test your deeptime installation but running the following in your environment:

python -c "import deeptime; print(deeptime.__version__)"

This should print the latest version of deeptime.

step 3: activate some helpers

In order to activate some features of the notebooks that we will be using, please also run

jupyter contrib nbextension install --sys-prefix
jupyter nbextension enable toc2/main
jupyter nbextension enable exercise2/main
jupyter nbextension enable nglview --py --sys-prefix

In case you are already a conda and jupyter notebook user with various environments, you can install your environment Python kernel via

python -m ipykernel install --user --name workshop

Sanity check

You can check whether you installed the correct versions by calling

conda list

PyEMMA should show up with version 2.5.11 and deeptime with version 0.4.1.

Usage

only on the first day

Please clone (download) this repository to get local access to the worksheets.

git clone https://github.com/markovmodel/pyemma-workshop.git

Please remember where on your local hard disk you have written it!

every morning:

activate environment (optional)

Skip if you don't know what a conda environment is. Only if conda environment is used; name might differ.

conda activate workshop

navigate to the right folder

Please navigate to the folder that you cloned from our github page.

cd path/to/pyemma-workshop/notebooks

start the jupyter notebook server

This command will start the notebook server:

jupyter notebook

Your browser should pop up pointing to a list of notebooks. If it's the wrong browser, add for example --browser=firefox or copy and paste the URL into the browser of your choice.

getting updates

Once you have a local clone of this repository, you can easily obtain updates with git pull. We'll let you know once we have published anything new. If you work directly in the notebooks that we provide, you might have to use the sequence (git pull will raise an error):

git stash
git pull
git stash pop